http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/RuntimeEnvironmentConstraint.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/RuntimeEnvironmentConstraint.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/RuntimeEnvironmentConstraint.java new file mode 100644 index 0000000..8324d61 --- /dev/null +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/RuntimeEnvironmentConstraint.java @@ -0,0 +1,160 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package org.apache.taverna.activities.externaltool.desc; + +import java.util.Collection; +import java.util.Iterator; + +import org.apache.log4j.Logger; + + +/** + * When use cases present a runtime environment, then they don't want to express + * that these would provide such, but that these request such, i.e. they constrain + * lists of potentially eligible queues. + * @author Steffen Moeller + * @since 2008 + */ +public class RuntimeEnvironmentConstraint extends RuntimeEnvironment { + + private static Logger logger = Logger.getLogger(RuntimeEnvironmentConstraint.class); + + private static String[] ACCEPTED_RELATIONS = new String[] {"=", ">=", "<=", ">", "<"}; + /** + * If there is no relation specified, presume >= + */ + private static String DEFAULT_RELATION = ">="; + + public static String[] getAcceptedRelations() { + return ACCEPTED_RELATIONS; + } + + public static String getDefaultRelation() { + return DEFAULT_RELATION; + } + + /** + * Identifies the relation between runtime environments to be tested + */ + protected String relation; + + /** + * Accessor function for relation + */ + public String getRelation() { + return this.relation; + } + + /** + * Tests of a relation is supported + * @param relation + * @return true iff in <, > , <=, >=, = + */ + public static boolean acceptedRelation(String relation) { + if ((null == relation) || relation.equals("")) { + return false; + } + return relation.equals("=")||relation.equals(">=")||relation.equals("<=")||relation.equals(">")||relation.equals("<"); + } + + /** + * Constructor + * @param id - expects the name of the runtime environment together with the version to which the + * @param relation - relates to (">","<","=",">=","<=") + */ + public RuntimeEnvironmentConstraint(String id, String relation) { + super(id); + if (null == relation || relation.equals("")) { + relation=RuntimeEnvironmentConstraint.getDefaultRelation(); + } + if (relation.equals("==")) { + relation="="; + } + else if (relation.equals("=<")) { + relation="<="; + } + else if (!RuntimeEnvironmentConstraint.acceptedRelation(relation)) { + logger.warn("Unknown relation '"+relation+"', presuming '"+RuntimeEnvironmentConstraint.getDefaultRelation()+"'"); + relation=RuntimeEnvironmentConstraint.getDefaultRelation(); + } + this.relation=relation; + } + + /** + * Perfoms test if the RuntimeEnvironment (RE) passed as argument fulfills the requirements set by the constraint. + * @param re - RE to test + * @return true iff the RE fulfills this REconstraint. + */ + public boolean isFulfilledBy(RuntimeEnvironment re) { + logger.info(re.getID()+" " + this.getRelation() + " "+this.getID() + " ?"); + if (this.getRelation().equals("=")) { + logger.info("="); + return re.getID().equals(this.getID()); + } + if (!re.getName().equals(this.getName())) { + logger.warn("Name match failed"); + return false; + } + int c = RuntimeEnvironment.compareVersions(re.getVersion(),this.getVersion()); + logger.info("c="+c); + if (this.getRelation().equals(">")) return c>0; + if (this.getRelation().equals(">=")) return c>=0; + if (this.getRelation().equals("<=")) return c<=0; + if (this.getRelation().equals("<")) return c<0; + throw new RuntimeException("Unknown/untreated releation '"+this.getRelation()+"'"); + } + + /** + * Iterates over all the RuntimeEnvironments passed as argument. + * @param REs - list of RuntimeEnvironments, mostly those offered at a particular queue + * @return true iff any RE among the REs passed as argument are fulfilling the constraint + */ + public boolean isFulfilledByAtLeastOneIn(Collection<RuntimeEnvironment> REs) { + boolean fulfilled = false; + Iterator<RuntimeEnvironment> i = REs.iterator(); + while(i.hasNext() && !fulfilled) { + RuntimeEnvironment r = i.next(); + fulfilled = this.isFulfilledBy(r); + } + return fulfilled; + } + /** + * For testing purposes + */ + public static void main(String argv[]) { + try { + if (argv[0].equals("--help") || argv.length != 3) { + logger.error("Expecting arguments (<|>|=|<=|>=) runtime1-version runtime2-version"); + } + else { + RuntimeEnvironmentConstraint r1 = new RuntimeEnvironmentConstraint(argv[1], argv[0]); + RuntimeEnvironment r2 = new RuntimeEnvironment(argv[2]); + logger.info("r1.getName(): "+r1.getName()); + logger.info("r1.getVersion(): "+r1.getVersion()); + logger.info("r1.getRelation(): "+r1.getRelation()); + logger.info("r2.getName(): "+r2.getName()); + logger.info("r2.getVersion(): "+r2.getVersion()); + logger.info("r1.isFulfilledBy(r2): "+String.valueOf(r1.isFulfilledBy(r2))); + } + } + catch (Exception e) { + logger.error(e); + } + } +}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInput.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInput.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInput.java new file mode 100644 index 0000000..3d68272 --- /dev/null +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInput.java @@ -0,0 +1,134 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package org.apache.taverna.activities.externaltool.desc; + +import java.nio.charset.Charset; + +import org.apache.taverna.activities.externaltool.ExternalToolActivity; +import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean; +import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty; + +/** + * Integrates inputs to the grid that come from the use case descriptions + * with those that are fed through the workflow. + * + * this class controls name and data storage of one input, + * no matter where the data comes from + */ +@ConfigurationBean(uri = ExternalToolActivity.URI + "#AbstractScriptInput") +public abstract class ScriptInput { + /** + * This input can be referenced under the name 'tag'. + */ + private String tag = null; + /** + * In most cases, the data will be stored under a specific + * filename. + */ + private boolean file = false; + /** + * Set, if the name of the file to be executed is not + * explicitly set but prepared by some automatism and referenced + * via the tagging principle. + */ + private boolean tempFile = false; + /** + * True if (!) the data is binary. (Text otherwise) + */ + private boolean binary = false; + + private String charsetName = Charset.defaultCharset().name(); + private boolean forceCopy = false; + + /** + * @return the tag + */ + public final String getTag() { + return tag; + } + /** + * @param tag the tag to set + */ + @ConfigurationProperty(name = "tag", label = "Tag") + public final void setTag(String tag) { + this.tag = tag; + } + /** + * @return the file + */ + public final boolean isFile() { + return file; + } + /** + * @param file the file to set + */ + @ConfigurationProperty(name = "file", label = "File") + public final void setFile(boolean file) { + this.file = file; + } + /** + * @return the tempFile + */ + public final boolean isTempFile() { + return tempFile; + } + /** + * @param tempFile the tempFile to set + */ + @ConfigurationProperty(name = "tempFile", label = "Temporary File") + public final void setTempFile(boolean tempFile) { + this.tempFile = tempFile; + } + /** + * @return the binary + */ + public final boolean isBinary() { + return binary; + } + /** + * @param binary the binary to set + */ + @ConfigurationProperty(name = "binary", label = "Binary") + public final void setBinary(boolean binary) { + this.binary = binary; + } + + public String getCharsetName() { + return this.charsetName; + } + /** + * @param charsetName the charsetName to set + */ + @ConfigurationProperty(name = "charsetName", label = "Chararter Set") + public void setCharsetName(String charsetName) { + this.charsetName = charsetName; + } + + @ConfigurationProperty(name = "forceCopy", label = "Force Copy") + public final void setForceCopy(boolean forceCopy) { + this.forceCopy = forceCopy; + + } + /** + * @return the forceCopy + */ + public boolean isForceCopy() { + return forceCopy; + } +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInputStatic.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInputStatic.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInputStatic.java new file mode 100644 index 0000000..78b6c3b --- /dev/null +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInputStatic.java @@ -0,0 +1,73 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package org.apache.taverna.activities.externaltool.desc; + +import org.apache.taverna.activities.externaltool.ExternalToolActivity; +import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean; +import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty; + +/** + * This subclass of script input is used to manage static content + * which is embedded into the use case description. + */ +@ConfigurationBean(uri = ExternalToolActivity.URI + "#ScriptInputStatic") +public class ScriptInputStatic extends ScriptInput { + + public ScriptInputStatic() { + } + + private String url = null; //if this is set, load content from remote URL + private String content = null; + + @Override + public String toString() { + return "InputStatic[tag: " + + getTag() + (isFile() ? ", file" : "") + (isTempFile() ? ", tempfile" : "") + (isBinary() ? ", binary" : "") + ", content: " + content + "]"; + } + + /** + * @return the url + */ + public final String getUrl() { + return url; + } + + /** + * @param url the url to set + */ + @ConfigurationProperty(name = "url", label = "URL", required=false) + public final void setUrl(String url) { + this.url = url; + } + + /** + * @return the content + */ + public final String getContent() { + return content; + } + + /** + * @param content the content to set + */ + @ConfigurationProperty(name = "content", label = "Content", required=false) + public final void setContent(String content) { + this.content = content; + } +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInputUser.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInputUser.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInputUser.java new file mode 100644 index 0000000..a74bb5d --- /dev/null +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInputUser.java @@ -0,0 +1,99 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package org.apache.taverna.activities.externaltool.desc; +import java.util.ArrayList; + +import org.apache.taverna.activities.externaltool.ExternalToolActivity; +import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean; +import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty; + +/** + * Internal description of output + */ +@ConfigurationBean(uri = ExternalToolActivity.URI + "#ScriptInput") +public class ScriptInputUser extends ScriptInput { + + /** + * This input may be fed from multiple ouputs. + */ + private boolean list = false; + /** + * True if the data from a list input in taverna is concatenated into one single input file. + */ + private boolean concatenate = false; + + private ArrayList<String> mime = new ArrayList<String>(); + + @Override + public String toString() { + return "Input[tag: " + getTag() + (isFile() ? ", file" : "") + + (isTempFile() ? ", tempfile" : "") + + (isBinary() ? ", binary" : "") + (list ? ", list" : "") + + (concatenate ? ", concatenate" : "") + + " mime: " + mime.toString() + "]"; + } + + /** + * @return the list + */ + public final boolean isList() { + return list; + } + + /** + * @param list the list to set + */ + @ConfigurationProperty(name = "list", label = "List") + public final void setList(boolean list) { + this.list = list; + } + + /** + * @return the concatenate + */ + public final boolean isConcatenate() { + return concatenate; + } + + /** + * @param concatenate the concatenate to set + */ + @ConfigurationProperty(name = "concatenate", label = "Concatenate") + public final void setConcatenate(boolean concatenate) { + this.concatenate = concatenate; + } + + /** + * @return the mime + */ + public final ArrayList<String> getMime() { + if (mime == null) { + mime = new ArrayList<String>(); + } + return mime; + } + + /** + * @param mime the mime to set + */ + @ConfigurationProperty(name = "mime", label = "Mime Types", required=false) + public final void setMime(ArrayList<String> mime) { + this.mime = mime; + } +}; http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptOutput.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptOutput.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptOutput.java new file mode 100644 index 0000000..77bbc83 --- /dev/null +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptOutput.java @@ -0,0 +1,88 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package org.apache.taverna.activities.externaltool.desc; +import java.util.ArrayList; + +import org.apache.taverna.activities.externaltool.ExternalToolActivity; +import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean; +import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty; + +/** + * Internal description of input + */ +@ConfigurationBean(uri = ExternalToolActivity.URI + "#ScriptOutput") +public class ScriptOutput { + private String path; + private boolean binary; + private ArrayList<String> mime = new ArrayList<String>(); + + @Override + public String toString() { + return "Output[path: " + path + (binary ? ", binary" : "") + + " mime: " + mime.toString() + "]"; + } + + /** + * @return the path + */ + public final String getPath() { + return path; + } + + /** + * @param path the path to set + */ + @ConfigurationProperty(name = "path", label = "Path") + public final void setPath(String path) { + this.path = path; + } + + /** + * @return the binary + */ + public final boolean isBinary() { + return binary; + } + + /** + * @param binary the binary to set + */ + @ConfigurationProperty(name = "binary", label = "Binary") + public final void setBinary(boolean binary) { + this.binary = binary; + } + + /** + * @return the mime + */ + public final ArrayList<String> getMime() { + if (mime == null) { + mime = new ArrayList<String>(); + } + return mime; + } + + /** + * @param mime the mime to set + */ + @ConfigurationProperty(name = "mime", label = "Mime Types", required=false) + public final void setMime(ArrayList<String> mime) { + this.mime = mime; + } +}; http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseDescription.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseDescription.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseDescription.java new file mode 100644 index 0000000..934330f --- /dev/null +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseDescription.java @@ -0,0 +1,897 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package org.apache.taverna.activities.externaltool.desc; + +import java.io.IOException; +import java.io.InputStream; +import java.net.MalformedURLException; +import java.net.URL; +import java.util.ArrayList; +import java.util.Collections; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Map.Entry; +import java.util.Set; + +import javax.swing.ImageIcon; + +import org.apache.taverna.activities.externaltool.ExternalToolActivity; +import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean; +import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty; +import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty.OrderPolicy; +import org.apache.taverna.workflowmodel.serialization.DeserializationException; +import org.apache.taverna.workflowmodel.utils.Tools; + +import org.apache.log4j.Logger; +import org.jdom.Document; +import org.jdom.Element; +import org.jdom.JDOMException; +import org.jdom.input.SAXBuilder; + +import org.apache.commons.lang.StringUtils; + +/** + * Class representation of XML-description of UseCases + */ +@ConfigurationBean(uri = ExternalToolActivity.URI + "#ToolDescription") +public class UseCaseDescription { + + private static Logger logger = Logger.getLogger(UseCaseDescription.class); + + /** + * Identifier for the retrieval of this UseCase in the sharedRepository + * database, respectively its XML export. + */ + private String usecaseid = ""; + /** + * Workflow Elements now can get a group identifier. There may be subgroups + * divided by : + */ + private String group = ""; + /** + * Textual description of the use case itself. This description is very + * short to fit on the single line that is prepared for such descriptions in + * the Taverna workflow element list. + */ + private String description = ""; + /** + * What is actually executed on the shell. + */ + private String command = ""; + + /** + * Accessor function of command + * + * @return shell-executable series of commands + */ + public String getCommand() { + if (null == command) { + // FIXME: Is this possible? + return ""; + } else { + return command; + } + } + + /** + * Routine that may be executed as a first check if the program is indeed + * installed. + */ + private String test_local = null; + + /** + * URL of an icon that would help users to recognise the use case + */ + private String icon_url = null; + + private int preparingTimeoutInSeconds = 20 * 60; // 20 minutes + private int executionTimeoutInSeconds = 30 * 60; // 30 minutes + + private List<String> tags = new ArrayList<String>(); + private List<RuntimeEnvironmentConstraint> REs = new ArrayList<RuntimeEnvironmentConstraint>(); + private ArrayList<String> queue_preferred = new ArrayList<String>(); + private ArrayList<String> queue_deny = new ArrayList<String>(); + + private List<ScriptInputStatic> static_inputs = new ArrayList<ScriptInputStatic>(); + private Map<String, ScriptInput> inputs = new HashMap<String, ScriptInput>(); + private Map<String, ScriptOutput> outputs = new HashMap<String, ScriptOutput>(); + + private boolean includeStdIn = false; + private boolean includeStdOut = true; + private boolean includeStdErr = true; + + private List<Integer> validReturnCodes = new ArrayList<Integer>(); + + /** + * Default constructor to make xstream happy + */ + public UseCaseDescription() { + + } + + /** + * Constructor, for special purpose usecases. + * + * @param usecaseid + */ + public UseCaseDescription(String usecaseid) { + this.setUsecaseid(usecaseid); + } + + /** + * Constructor, expects an input stream containing the xml. for example, use + * getClass().getClassLoader().getResourceAsStream("..") to load a usecase + * from your program jar + */ + public UseCaseDescription(InputStream programAsStream) throws DeserializationException { + SAXBuilder builder = new SAXBuilder(); + Document doc; + try { + doc = builder.build(programAsStream); + programAsStream.close(); + } catch (JDOMException e) { + throw new DeserializationException("Error deserializing usecase", e); + } catch (IOException e) { + throw new DeserializationException("Error deserializing usecase", e); + } + readFromXmlElement(doc.getRootElement()); + } + + /** + * Constructor, expects an XML-root to dissect. + */ + public UseCaseDescription(Element programNode) throws DeserializationException { + readFromXmlElement(programNode); + } + +/** + * Produce an XML description of the UseCaseDescription + */ + public Element writeToXMLElement() { + Element programNode = new Element("program"); + programNode.setAttribute("name", getUsecaseid()); + programNode.setAttribute("description", getDescription()); + // Always use element version of command +// programNode.setAttribute("command", getCommand()); + Element commandNode = new Element("command"); + commandNode.addContent(getCommand()); + programNode.addContent(commandNode); + programNode.setAttribute("timeout", Integer.toString(getExecutionTimeoutInSeconds())); + programNode.setAttribute("preparing_timeout", Integer.toString(getPreparingTimeoutInSeconds())); + programNode.setAttribute("includeStdIn", Boolean.toString(isIncludeStdIn())); + programNode.setAttribute("includeStdOut", Boolean.toString(isIncludeStdOut())); + programNode.setAttribute("includeStdErr", Boolean.toString(isIncludeStdErr())); + for (ScriptInputStatic si : getStatic_inputs()) { + Element staticNode = new Element("static"); + if (si.isBinary()) { + staticNode.setAttribute("binary", "true"); + } + if (si.isForceCopy()) { + staticNode.setAttribute("forceCopy", "true"); + } + if (si.isFile()) { + Element fileNode = new Element("file"); + fileNode.setAttribute("path", si.getTag()); + staticNode.addContent(fileNode); + } else if (si.isTempFile()) { + Element tempfileNode = new Element("tempfile"); + tempfileNode.setAttribute("tag", si.getTag()); + staticNode.addContent(tempfileNode); + } else { + Element replaceNode = new Element("replace"); + replaceNode.setAttribute("tag", si.getTag()); + staticNode.addContent(replaceNode); + } + if (si.getUrl() != null) { + Element contentNode = new Element("content"); + contentNode.setAttribute("url", si.getUrl()); + staticNode.addContent(contentNode); + } else { + Element contentNode = new Element("content"); + contentNode.addContent((String) si.getContent()); + staticNode.addContent(contentNode); + } + programNode.addContent(staticNode); + } + for (Entry<String, ScriptInput> entry : getInputs().entrySet()) { + String name = entry.getKey(); + ScriptInputUser si = (ScriptInputUser) entry.getValue(); + Element inputNode = new Element("input"); + inputNode.setAttribute("name", name); + if (si.isBinary()) { + inputNode.setAttribute("binary", "true"); + } + if (si.isForceCopy()) { + inputNode.setAttribute("forceCopy", "true"); + } + if (si.isConcatenate()) { + inputNode.setAttribute("concatenate", "true"); + } + if (si.isList()) { + inputNode.setAttribute("list", "true"); + } + if (si.isFile()) { + Element fileNode = new Element("file"); + fileNode.setAttribute("path", si.getTag()); + inputNode.addContent(fileNode); + } else if (si.isTempFile()) { + Element tempfileNode = new Element("tempfile"); + tempfileNode.setAttribute("tag", si.getTag()); + inputNode.addContent(tempfileNode); + } else { + Element replaceNode = new Element("replace"); + replaceNode.setAttribute("tag", si.getTag()); + inputNode.addContent(replaceNode); + } + for (String mime : si.getMime()) { + Element mimeNode = new Element("mime"); + mimeNode.setAttribute("type", mime); + inputNode.addContent(mimeNode); + } + programNode.addContent(inputNode); + } + for (Entry<String, ScriptOutput> entry : getOutputs().entrySet()) { + String name = entry.getKey(); + ScriptOutput so = entry.getValue(); + Element outputNode = new Element("output"); + outputNode.setAttribute("name", name); + if (so.isBinary()) { + outputNode.setAttribute("binary", "true"); + } + Element fromfileNode = new Element("fromfile"); + fromfileNode.setAttribute("path", so.getPath()); + outputNode.addContent(fromfileNode); + for (String mime : so.getMime()) { + Element mimeNode = new Element("mime"); + mimeNode.setAttribute("type", mime); + outputNode.addContent(mimeNode); + } + programNode.addContent(outputNode); + } + for (RuntimeEnvironmentConstraint rec : getREs()) { + Element rteNode = new Element("rte"); + rteNode.setAttribute("name", rec.getID()); + rteNode.setAttribute("relation", rec.getRelation()); + programNode.addContent(rteNode); + } + if ((group != null) && !group.isEmpty()) { + Element groupNode = new Element("group"); + groupNode.setAttribute("name", group); + programNode.addContent(groupNode); + } + if ((test_local != null) && !test_local.isEmpty()) { + Element testNode = new Element("test"); + testNode.setAttribute("local", test_local); + programNode.addContent(testNode); + } + if ((icon_url != null) && !icon_url.isEmpty()) { + Element iconNode = new Element("icon"); + iconNode.setAttribute("url", icon_url); + programNode.addContent(iconNode); + } + if (!getQueue_preferred().isEmpty() || !getQueue_deny().isEmpty()) { + Element queueNode = new Element("queue"); + for (String url : getQueue_preferred()) { + Element preferredNode = new Element("prefer"); + preferredNode.setAttribute("url", url); + queueNode.addContent(preferredNode); + } + for (String url : getQueue_deny()) { + Element denyNode = new Element("deny"); + denyNode.setAttribute("url", url); + queueNode.addContent(denyNode); + } + programNode.addContent(queueNode); + } + Element validReturnCodesNode = new Element("validReturnCodes"); + validReturnCodesNode.setAttribute("codes", getReturnCodesAsText()); + programNode.addContent(validReturnCodesNode); + + return programNode; + } + /** + * Specifies the UseCaseDescription from the root of an XML description + * which is accessible online. + * + * @param programNode + * @throws DeserializationException + */ + private void readFromXmlElement(Element programNode) throws DeserializationException { + if (programNode.getName().compareToIgnoreCase("program") != 0) + throw new DeserializationException("Expected <program>, read '" + programNode.getName() + "'"); + + setUsecaseid(programNode.getAttributeValue("name")); + setDescription(programNode.getAttributeValue("description")); + setCommand(programNode.getAttributeValue("command")); + String timeoutStr = programNode.getAttributeValue("timeout"); + if (timeoutStr != null) + setExecutionTimeoutInSeconds(Integer.parseInt(timeoutStr)); + timeoutStr = programNode.getAttributeValue("preparing_timeout"); + if (timeoutStr != null) + setPreparingTimeoutInSeconds(Integer.parseInt(timeoutStr)); + + String includeStdInStr = programNode.getAttributeValue("includeStdIn"); + if (includeStdInStr != null && !includeStdInStr.isEmpty()) { + setIncludeStdIn(includeStdInStr.equals("true")); + } + + String includeStdOutStr = programNode.getAttributeValue("includeStdOut"); + if (includeStdOutStr != null && !includeStdOutStr.isEmpty()) { + setIncludeStdOut(includeStdOutStr.equals("true")); + } + + String includeStdErrStr = programNode.getAttributeValue("includeStdErr"); + if (includeStdErrStr != null && !includeStdErrStr.isEmpty()) { + setIncludeStdErr(includeStdErrStr.equals("true")); + } + + for (Object cur_ob : programNode.getChildren()) { + Element cur = (Element) cur_ob; + + String name = cur.getAttributeValue("name"); + + String type = cur.getName(); + boolean binary = false; + if (null != cur.getAttributeValue("binary") && cur.getAttributeValue("binary").equalsIgnoreCase("true")) { + binary = true; + } + boolean list = false; + if (null != cur.getAttributeValue("list") && cur.getAttributeValue("list").equalsIgnoreCase("true")) { + list = true; + } + boolean concatenate = false; + if (null != cur.getAttributeValue("concatenate") && cur.getAttributeValue("concatenate").equalsIgnoreCase("true")) { + concatenate = true; + } + boolean forceCopy = false; + if (null != cur.getAttributeValue("forceCopy") && cur.getAttributeValue("forceCopy").equalsIgnoreCase("true")) { + forceCopy = true; + } + + Element inner = null; + String innerType = null, tag = null, path = null; + if (cur.getChildren().size() > 0) { + inner = (Element) cur.getChildren().get(0); + innerType = inner.getName(); + tag = inner.getAttributeValue("tag"); + path = inner.getAttributeValue("path"); + } + // build mime type declaration list + ArrayList<String> mime = new ArrayList<String>(); + for (Object child : cur.getChildren()) { + Element curChild = (Element) child; + if (curChild.getName().equalsIgnoreCase("mime")) { + mime.add(curChild.getAttributeValue("type")); + } + } + if (type.equalsIgnoreCase("static")) { + ScriptInputStatic si = new ScriptInputStatic(); + Element content = cur.getChild("content"); + if (content == null) + throw new DeserializationException("FIXME: script tag without embedded content tag"); + si.setUrl(content.getAttributeValue("url")); + if (si.getUrl() == null) + si.setContent(content.getText()); + fillInputDescription(si, binary, forceCopy, innerType, tag, path); + getStatic_inputs().add(si); + } else if (type.equalsIgnoreCase("input")) { + ScriptInputUser indesc = new ScriptInputUser(); + indesc.setList(list); + indesc.setMime(mime); + indesc.setConcatenate(concatenate); + fillInputDescription(indesc, binary, forceCopy, innerType, tag, path); + getInputs().put(Tools.sanitiseName(name), indesc); + } else if (type.equalsIgnoreCase("output")) { + ScriptOutput outdesc = new ScriptOutput(); + outdesc.setMime(mime); + + boolean ok = true; + if (null == innerType) { + // don't know what to do + throw new DeserializationException("FIXME: Found null == innerType for output, is this the bug?"); + } else if (innerType.equalsIgnoreCase("fromfile")) { + outdesc.setPath(path); + outdesc.setBinary(binary); + } else { + throw new DeserializationException("Problem reading output port: unknown innerType '" + innerType + "'"); + } + if (ok) { + getOutputs().put(Tools.sanitiseName(name), outdesc); + } + } else if (type.equalsIgnoreCase("rte") || type.equalsIgnoreCase("re")) { + getREs().add(new RuntimeEnvironmentConstraint(name, cur.getAttributeValue("relation"))); + } else if (type.equalsIgnoreCase("group")) { + group = name; + } else if (type.equalsIgnoreCase("test")) { + test_local = cur.getAttributeValue("local"); + } else if (type.equalsIgnoreCase("icon")) { + icon_url = cur.getAttributeValue("url"); + } else if (type.equalsIgnoreCase("queue")) { + for (Object child_ob : cur.getChildren()) { + Element child = (Element) child_ob; + if (child.getName().equalsIgnoreCase("prefer")) + getQueue_preferred().add(child.getAttributeValue("url")); + else if (child.getName().equalsIgnoreCase("deny")) + getQueue_deny().add(child.getAttributeValue("url")); + else + throw new DeserializationException("Error while reading usecase " + this.getUsecaseid() + ": invalid queue entry"); + } + } else if (type.equalsIgnoreCase("command")) { + // i like to have the ability to inject complete shell script + // fragments into the use case, + // so this should be replace and should allow multiple lines + if ((getCommand() != null) && !getCommand().isEmpty()) { + throw new DeserializationException("You have specified both command attribute and command tag."); + } + setCommand(cur.getText()); + } else if (type.equalsIgnoreCase("validReturnCodes")) { + String codeString = cur.getAttributeValue("codes"); + if (codeString != null) { + setReturnCodesAsText(codeString); + } + } + else { + throw new DeserializationException("Unexpected and uninterpreted attribute " + type); + } + } + } + + private void fillInputDescription(ScriptInput fillMe, boolean binary, boolean forceCopy, String innerType, String tag, String path) throws DeserializationException { + fillMe.setBinary(binary); + fillMe.setForceCopy(forceCopy); + if (null == innerType) { + // don't know what to do + throw new DeserializationException("FIXME: Found null == innerType for input, is this the bug?"); + } else if (innerType.equalsIgnoreCase("replace")) { + fillMe.setTag(tag); + fillMe.setTempFile(false); + fillMe.setFile(false); + getTags().add(tag); + } else if (innerType.equalsIgnoreCase("tempfile")) { + fillMe.setTag(tag); + fillMe.setTempFile(true); + fillMe.setFile(false); + getTags().add(tag); + } else if (innerType.equalsIgnoreCase("file")) { + fillMe.setTag(path); + fillMe.setTempFile(false); + fillMe.setFile(true); + } else { + throw new DeserializationException("Problem reading input port: unknown innerType '" + innerType + "'"); + } + } + + /** + * returns icon that is referenced in use case description + */ + public ImageIcon getImageIcon() { + if (null == icon_url) return null; + try { + URL u = new URL(icon_url); + return new ImageIcon(u, getUsecaseid()); + } catch (Exception e) { + logger.error(e); + return null; + } + } + + /** + * String representation of the use case. It also contains interesting + * information on the availability of resources in the grid to actually + * execute that workflow element. + * + * @return String + */ + @Override + public String toString() { + List<String> hlp = new ArrayList<String>(); + hlp.add("usecaseid: " + getUsecaseid()); + hlp.add("description: " + getDescription()); + hlp.add("group: " + group); + hlp.add("test: " + test_local); + hlp.add("tags: " + getTags()); + for (Map.Entry<String, ScriptInput> cur : getInputs().entrySet()) { + hlp.add(">" + cur.getKey() + ">: " + cur.getValue().toString()); + } + for (Map.Entry<String, ScriptOutput> cur : getOutputs().entrySet()) { + hlp.add("<" + cur.getKey() + "<: " + cur.getValue().toString()); + } + hlp.add("RE: " + getREs().toString()); + hlp.add("preferred queues: " + getQueue_preferred()); + hlp.add("denied queues: " + getQueue_deny()); + String tos = super.toString() + "["; + for (int i = 0; i < hlp.size(); i++) { + if (i != 0) + tos += ", "; + tos += hlp.get(i); + } + return tos + " ]"; + } + + /** + * hajo's test just pass an url or file url to an xml file + * + * @throws IOException + * @throws MalformedURLException + * @throws DeserializationException + */ + public static void main(String[] argv) throws MalformedURLException, IOException, DeserializationException { + UseCaseDescription d = new UseCaseDescription(new URL(argv[0]).openStream()); + logger.info(d.getCommand()); + } + + /** + * @param command the command to set + */ + @ConfigurationProperty(name = "command", label = "Command", description="What is actually executed on the shell") + public void setCommand(String command) { + this.command = command; + } + + /** + * @param description the description to set + */ + @ConfigurationProperty(name = "description", label = "Description", description="Textual description of the tool", required=false, uri="http://purl.org/dc/elements/1.1/description";) + public void setDescription(String description) { + this.description = description; + } + + /** + * @return the description + */ + public String getDescription() { + return description; + } + + /** + * @param executionTimeoutInSeconds the executionTimeoutInSeconds to set + */ + @ConfigurationProperty(name = "executionTimeoutInSeconds", label = "Execution Timeout In Seconds") + public void setExecutionTimeoutInSeconds(int executionTimeoutInSeconds) { + this.executionTimeoutInSeconds = executionTimeoutInSeconds; + } + + /** + * @return the executionTimeoutInSeconds + */ + public int getExecutionTimeoutInSeconds() { + return executionTimeoutInSeconds; + } + + /** + * @param inputs the inputs to set + */ + public void setInputs(Map<String, ScriptInput> inputs) { + this.inputs = inputs; + } + + @ConfigurationProperty(name = "inputs", label = "Inputs", required=false) + public void setInputs(Set<InputMap> inputs) { + if (inputs != null) { + this.inputs = new HashMap<String, ScriptInput>(); + for (InputMap inputMap : inputs) { + this.inputs.put(inputMap.getPort(), inputMap.getInput()); + } + } else { + this.inputs = null; + } + } + + /** + * @return the inputs + */ + public Map<String, ScriptInput> getInputs() { + if (inputs == null) { + inputs = new HashMap<String, ScriptInput>(); + } + return inputs; + } + + /** + * @param outputs the outputs to set + */ + public void setOutputs(Map<String, ScriptOutput> outputs) { + this.outputs = outputs; + } + + @ConfigurationProperty(name = "outputs", label = "Outputs", required=false) + public void setOutputs(Set<OutputMap> outputs) { + if (outputs != null) { + this.outputs = new HashMap<String, ScriptOutput>(); + for (OutputMap outputMap : outputs) { + this.outputs.put(outputMap.getPort(), outputMap.getOutput()); + } + } else { + this.outputs = null; + } + } + + /** + * @return the outputs + */ + public Map<String, ScriptOutput> getOutputs() { + if (outputs == null) { + outputs = new HashMap<String, ScriptOutput>(); + } + return outputs; + } + + /** + * @param preparingTimeoutInSeconds the preparingTimeoutInSeconds to set + */ + @ConfigurationProperty(name = "preparingTimeoutInSeconds", label = "Preparing Timeout In Seconds") + public void setPreparingTimeoutInSeconds(int preparingTimeoutInSeconds) { + this.preparingTimeoutInSeconds = preparingTimeoutInSeconds; + } + + /** + * @return the preparingTimeoutInSeconds + */ + public int getPreparingTimeoutInSeconds() { + return preparingTimeoutInSeconds; + } + + /** + * @param queue_deny the queue_deny to set + */ + public void setQueue_deny(ArrayList<String> queue_deny) { + this.queue_deny = queue_deny; + } + + /** + * @return the queue_deny + */ + public ArrayList<String> getQueue_deny() { + if (queue_deny == null) { + queue_deny = new ArrayList<String>(); + } + return queue_deny; + } + + /** + * @param queue_preferred the queue_preferred to set + */ + public void setQueue_preferred(ArrayList<String> queue_preferred) { + this.queue_preferred = queue_preferred; + } + + /** + * @return the queue_preferred + */ + public ArrayList<String> getQueue_preferred() { + if (queue_preferred == null) { + queue_preferred = new ArrayList<String>(); + } + return queue_preferred; + } + + /** + * @param rEs the rEs to set + */ + public void setREs(List<RuntimeEnvironmentConstraint> rEs) { + REs = rEs; + } + + /** + * @return the rEs + */ + public List<RuntimeEnvironmentConstraint> getREs() { + if (REs == null) { + REs = new ArrayList<RuntimeEnvironmentConstraint>(); + } + return REs; + } + + /** + * @param static_inputs the static_inputs to set + */ + @ConfigurationProperty(name = "staticInputs", label = "Static Inputs", ordering=OrderPolicy.NON_ORDERED, required=false) + public void setStatic_inputs(List<ScriptInputStatic> static_inputs) { + this.static_inputs = static_inputs; + } + + /** + * @return the static_inputs + */ + public List<ScriptInputStatic> getStatic_inputs() { + if (static_inputs == null) { + static_inputs = new ArrayList<ScriptInputStatic>(); + } + return static_inputs; + } + + /** + * @param tags the tags to set + */ + public void setTags(List<String> tags) { + this.tags = tags; + } + + /** + * @return the tags + */ + public List<String> getTags() { + if (tags == null) { + tags = new ArrayList<String>(); + } + return tags; + } + + /** + * @param usecaseid the usecaseid to set + */ + @ConfigurationProperty(name = "usecaseid", label = "Title", uri="http://purl.org/dc/elements/1.1/title";, required=false) + public void setUsecaseid(String usecaseid) { + this.usecaseid = usecaseid; + } + + /** + * @return the usecaseid + */ + public String getUsecaseid() { + return usecaseid; + } + + public boolean isIncludeStdIn() { + return includeStdIn; + } + + @ConfigurationProperty(name = "includeStdIn", label = "Include STDIN") + public void setIncludeStdIn(boolean includeStdIn) { + this.includeStdIn = includeStdIn; + } + + public boolean isIncludeStdOut() { + return includeStdOut; + } + + @ConfigurationProperty(name = "includeStdOut", label = "Include STDOUT") + public void setIncludeStdOut(boolean includeStdOut) { + this.includeStdOut = includeStdOut; + } + + public boolean isIncludeStdErr() { + return includeStdErr; + } + + @ConfigurationProperty(name = "includeStdErr", label = "Include STDERR") + public void setIncludeStdErr(boolean includeStdErr) { + this.includeStdErr = includeStdErr; + } + + /** + * @return the validReturnCodes + */ + public List<Integer> getValidReturnCodes() { + if (validReturnCodes == null) { + validReturnCodes = new ArrayList<Integer>(); + } + if (validReturnCodes.isEmpty()) { + validReturnCodes.add(0); + } + return validReturnCodes; + } + + /** + * @param validReturnCodes the validReturnCodes to set + */ + public void setValidReturnCodes(List<Integer> validReturnCodes) { + this.validReturnCodes = validReturnCodes; + } + + public String getReturnCodesAsText() { + return StringUtils.join(getValidReturnCodes(), ","); + } + + public void setReturnCodesAsText(String text) { + if (getValidReturnCodes() == null) { + validReturnCodes = new ArrayList<Integer>(); + } + validReturnCodes.clear(); + String[] codes = text.split(","); + for (String code : codes) { + try { + Integer codeInt = new Integer(code); + if (!validReturnCodes.contains(codeInt)) { + validReturnCodes.add(codeInt); + } + } + catch (NumberFormatException e) { + logger.error(e); + } + } + if (validReturnCodes.isEmpty()) { + validReturnCodes.add(0); + } + Collections.sort(validReturnCodes); + } + + /** + * @return the group + */ + public String getGroup() { + return group; + } + + /** + * @param group the group to set + */ + public void setGroup(String group) { + this.group = group; + } + + /** + * @return the icon_url + */ + public String getIcon_url() { + return icon_url; + } + + @ConfigurationBean(uri = ExternalToolActivity.URI + "#OutputMap") + public static class OutputMap { + private String port; + + private ScriptOutput output; + + public String getPort() { + return port; + } + + @ConfigurationProperty(name = "port", label = "Port") + public void setPort(String port) { + this.port = port; + } + + public ScriptOutput getOutput() { + return output; + } + + @ConfigurationProperty(name = "output", label = "Output") + public void setOutput(ScriptOutput output) { + this.output = output; + } + } + + @ConfigurationBean(uri = ExternalToolActivity.URI + "#InputMap") + public static class InputMap { + private String port; + + private ScriptInputUser input; + + public String getPort() { + return port; + } + + @ConfigurationProperty(name = "port", label = "Port") + public void setPort(String port) { + this.port = port; + } + + public ScriptInputUser getInput() { + return input; + } + + @ConfigurationProperty(name = "input", label = "Input") + public void setInput(ScriptInputUser input) { + this.input = input; + } + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseEnumeration.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseEnumeration.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseEnumeration.java new file mode 100644 index 0000000..1a43461 --- /dev/null +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseEnumeration.java @@ -0,0 +1,111 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package org.apache.taverna.activities.externaltool.desc; + +import java.io.IOException; +import java.io.InputStream; +import java.net.URL; +import java.net.URLConnection; +import java.util.ArrayList; +import java.util.List; + +import org.apache.taverna.workflowmodel.serialization.DeserializationException; + +import org.apache.log4j.Logger; +import org.jdom.Document; +import org.jdom.Element; +import org.jdom.JDOMException; +import org.jdom.input.SAXBuilder; + +public class UseCaseEnumeration { + + private static Logger logger = Logger.getLogger(UseCaseEnumeration.class); + + public static List<UseCaseDescription> readDescriptionsFromUrl(String xmlFileUrl) throws IOException { + + List<UseCaseDescription> ret = new ArrayList<UseCaseDescription>(); + URLConnection con = null; + try { + URL url = new URL(xmlFileUrl); + + con = url.openConnection(); + con.setConnectTimeout(4000); + ret = readDescriptionsFromStream(con.getInputStream()); + + } catch (IOException ioe) { + logger.error("Problem retrieving from " + xmlFileUrl); + logger.error(ioe); + throw ioe; + } + finally { + + } + + return ret; + + } + + public static List<UseCaseDescription> readDescriptionsFromStream(InputStream is) { + + List<UseCaseDescription> ret = new ArrayList<UseCaseDescription>(); + + SAXBuilder builder = new SAXBuilder(); + Document doc = null; + try { + doc = builder.build(is); + is.close(); + } catch (JDOMException e1) { + logger.error(e1); + return ret; + } catch (IOException e1) { + logger.error(e1); + return ret; + } finally { + try { + is.close(); + } catch (IOException e) { + logger.error(e); + } + } + + Element usecases = doc.getRootElement(); + for (Object ochild : usecases.getChildren()) { + Element child = (Element) ochild; + if (child.getName().equalsIgnoreCase("program")) { + try { + ret.add(new UseCaseDescription(child)); + } catch (DeserializationException e) { + logger.error(e); + } + } + } + return ret; + } + + public static UseCaseDescription readDescriptionFromUrl( + String repositoryUrl, String id) throws IOException { + List<UseCaseDescription> descriptions = readDescriptionsFromUrl(repositoryUrl); + for (UseCaseDescription usecase : descriptions) { + if (usecase.getUsecaseid().equals(id)) { + return usecase; + } + } + return null; + } +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/gui/AskUserForPwPopup.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/gui/AskUserForPwPopup.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/gui/AskUserForPwPopup.java new file mode 100644 index 0000000..9dbe959 --- /dev/null +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/gui/AskUserForPwPopup.java @@ -0,0 +1,74 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.taverna.activities.externaltool.gui; + +import javax.swing.JOptionPane; + +import org.apache.taverna.activities.externaltool.invocation.AskUserForPw; +import org.apache.taverna.activities.externaltool.ssh.SshNode; + +public final class AskUserForPwPopup implements AskUserForPw { + private SshNode ret; + private String pw, pp, kf, us; + + public static String ask(String message, String title) { + return (String) JOptionPane.showInputDialog(null, message, title, JOptionPane.QUESTION_MESSAGE, null, null, ""); + } + + public static boolean askYN(String message, String title) { + return JOptionPane.showConfirmDialog(null, message, title, JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE) == JOptionPane.YES_OPTION; + } + + public String getPassword() { + getUsername(); + if (pw != null) + return pw; + pw = ask("Please enter your password for " + us + " @ " + ret.getHost(), us + " @ " + ret.getHost()); + return pw; + } + + public String getPassphrase() { + getUsername(); + if (pp != null) + return pp; + pp = ask("Please enter your passphrase for " + kf + " used for " + us + " @ " + ret.getHost(), us + " @ " + ret.getHost()); + return pp; + } + + public String getKeyfile() { + getUsername(); + if (kf != null) + return kf; + kf = ask("Please enter the keyfile for " + us + " @ " + ret.getHost(), us + " @ " + ret.getHost()); + return kf; + } + + public String getUsername() { + if (us != null) + return us; + us = ask("Please enter the username for " + ret.getHost(), "Username for " + ret.getHost()); + return us; + } + + public void setSshNode(SshNode sshNode) { + this.ret = sshNode; + } + + public void authenticationSucceeded() { + } +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/gui/PleaseWaitDialog.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/gui/PleaseWaitDialog.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/gui/PleaseWaitDialog.java new file mode 100755 index 0000000..9e265c8 --- /dev/null +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/gui/PleaseWaitDialog.java @@ -0,0 +1,73 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package org.apache.taverna.activities.externaltool.gui; + +import java.util.ArrayList; +import java.util.List; + +import javax.swing.JDialog; +import javax.swing.JLabel; + +public class PleaseWaitDialog extends JDialog { + private static final long serialVersionUID = 1L; + + static PleaseWaitDialog instance = new PleaseWaitDialog(); + + public class WaitMessage{ + public WaitMessage() { + } + + String str; + public void set(String newstr) { + synchronized (PleaseWaitDialog.instance) { + if(this.str != null && this.str.equals(newstr)) return; + if(this.str != null) messages.remove(this.str); + this.str = newstr; + if(this.str != null) messages.add(this.str); + } + updateDialog(); + } + public void done() { + set(null); + } + } + + private void updateDialog() { + synchronized (PleaseWaitDialog.instance) { + if(messages.size() > 0) this.setVisible(true); + else this.setVisible(false); + String t = ""; + for (String cur : messages) { + t += cur + "<br>"; + } + l.setText("<html>"+t+"</html>"); + } + } + + List<String> messages = new ArrayList<String>(); + + JLabel l; + private PleaseWaitDialog() { + this.setAlwaysOnTop(true); + this.setTitle("Please wait"); + l = new JLabel(""); + this.add(l); + this.setSize(400, 100); + } +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/AskUserForPw.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/AskUserForPw.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/AskUserForPw.java new file mode 100644 index 0000000..04bced0 --- /dev/null +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/AskUserForPw.java @@ -0,0 +1,32 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package org.apache.taverna.activities.externaltool.invocation; + +public interface AskUserForPw { + + // we will try keyfile first + public String getKeyfile(); + public String getPassphrase(); + + // then username+password + public String getUsername(); + public String getPassword(); + + public void authenticationSucceeded(); +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/InvocationException.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/InvocationException.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/InvocationException.java new file mode 100644 index 0000000..d9f6bce --- /dev/null +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/InvocationException.java @@ -0,0 +1,36 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package org.apache.taverna.activities.externaltool.invocation; + +public class InvocationException extends Exception { + + /** + * + */ + private static final long serialVersionUID = 437316164959631591L; + + public InvocationException(String string) { + super(string); + } + + public InvocationException(Exception e) { + super(e); + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/UseCaseInvocation.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/UseCaseInvocation.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/UseCaseInvocation.java new file mode 100644 index 0000000..4d97030 --- /dev/null +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/UseCaseInvocation.java @@ -0,0 +1,321 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package org.apache.taverna.activities.externaltool.invocation; + +import java.io.BufferedWriter; +import java.io.ByteArrayOutputStream; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.io.OutputStreamWriter; +import java.net.MalformedURLException; +import java.net.URL; +import java.util.HashMap; +import java.util.List; +import java.util.Set; + +import org.apache.commons.io.IOUtils; +import org.apache.taverna.activities.externaltool.desc.ScriptInput; +import org.apache.taverna.activities.externaltool.desc.ScriptInputStatic; +import org.apache.taverna.activities.externaltool.desc.ScriptInputUser; +import org.apache.taverna.activities.externaltool.desc.UseCaseDescription; +import org.apache.taverna.invocation.InvocationContext; +import org.apache.taverna.reference.ExternalReferenceSPI; +import org.apache.taverna.reference.Identified; +import org.apache.taverna.reference.IdentifiedList; +import org.apache.taverna.reference.ReferenceService; +import org.apache.taverna.reference.ReferenceServiceException; +import org.apache.taverna.reference.ReferenceSet; +import org.apache.taverna.reference.T2Reference; +import org.apache.taverna.reference.impl.external.object.InlineByteArrayReferenceBuilder; +import org.apache.taverna.reference.impl.external.object.InlineStringReferenceBuilder; + +/** + * An abstraction of various forms to bring job using the software that is + * referenced as a use case towards their execution. + * + * @author Hajo Nils Krabbenhoeft with some contribution by + * @author Steffen Moeller + */ +public abstract class UseCaseInvocation { + + private String runId; + + + protected static String getActualOsCommand(String osCommand, String pathToOriginal, + String targetName, String pathTarget) { + String actualOsCommand = osCommand; + actualOsCommand = actualOsCommand.replace("%%PATH_TO_ORIGINAL%%", pathToOriginal); + actualOsCommand = actualOsCommand.replace("%%TARGET_NAME%%", targetName); + actualOsCommand = actualOsCommand.replace("%%PATH_TO_TARGET%%", pathTarget); + return actualOsCommand; + } + + protected UseCaseDescription usecase; + protected final HashMap<String, String> tags = new HashMap<String, String>(); + protected int nTempFiles = 0; + private static int submissionID = 0; + protected static InlineByteArrayReferenceBuilder inlineByteArrayReferenceBuilder = new InlineByteArrayReferenceBuilder(); + protected static InlineStringReferenceBuilder inlineStringReferenceBuilder = new InlineStringReferenceBuilder(); + private InvocationContext invocationContext; + private boolean retrieveData; + + /* + * get the class of the data we expect for a given input + */ + @SuppressWarnings("unchecked") + public Class getType(String inputName) { + if (!usecase.getInputs().containsKey(inputName)) + return null; + ScriptInputUser input = (ScriptInputUser) usecase.getInputs().get(inputName); + if (input.isList()) { + if (input.isBinary()) + return List.class; + else + return List.class; + } else { + if (input.isBinary()) + return byte[].class; + else + return String.class; + } + } + + /* + * get a list of all the input port names + */ + public Set<String> getInputs() { + return usecase.getInputs().keySet(); + } + + + /* + * get a id, incremented with each job. thus, this should be thread-wide + * unique + */ + public synchronized int getSubmissionID() { + return submissionID++; + } + + /* + * set the data for the input port with given name + */ + @SuppressWarnings("unchecked") + public void setInput(String inputName, ReferenceService referenceService, T2Reference t2Reference) throws InvocationException { + if (t2Reference == null) { + throw new InvocationException("No input specified for " + inputName); + } + ScriptInputUser input = (ScriptInputUser) usecase.getInputs().get(inputName); + if (input.isList()) { + IdentifiedList<T2Reference> listOfReferences = (IdentifiedList<T2Reference>) referenceService + .getListService().getList(t2Reference); + + if (!input.isConcatenate()) { + // this is a list input (not concatenated) + // so write every element to its own temporary file + // and create a filelist file + + // we need to write the list elements to temporary files + ScriptInputUser listElementTemp = new ScriptInputUser(); + listElementTemp.setBinary(input.isBinary()); + listElementTemp.setTempFile(true); + + String lineEndChar = "\n"; + if (!input.isFile() && !input.isTempFile()) { + lineEndChar = " "; + } + + String listFileContent = ""; + String filenamesFileContent = ""; + // create a list of all temp file names + for (T2Reference cur : listOfReferences) { + String tmp = setOneInput(referenceService, cur, + listElementTemp); + listFileContent += tmp + lineEndChar; + int ind = tmp.lastIndexOf('/'); + if (ind == -1) { + ind = tmp.lastIndexOf('\\'); + } + if (ind != -1) { + tmp = tmp.substring(ind + 1); + } + filenamesFileContent += tmp + lineEndChar; + } + + // how do we want the listfile to be stored? + ScriptInputUser listFile = new ScriptInputUser(); + listFile.setBinary(false); // since its a list file + listFile.setFile(input.isFile()); + listFile.setTempFile(input.isTempFile()); + listFile.setTag(input.getTag()); + T2Reference listFileContentReference = referenceService + .register(listFileContent, 0, true, invocationContext); + + tags.put(listFile.getTag(), setOneInput(referenceService, + listFileContentReference, listFile)); + + listFile.setTag(input.getTag() + "_NAMES"); + T2Reference filenamesFileContentReference = referenceService + .register(filenamesFileContent, 0, true, null); + tags.put(listFile.getTag(), setOneInput(referenceService, + filenamesFileContentReference, listFile)); + } else { + try { + // first, concatenate all data + if (input.isBinary()) { + ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); + BufferedWriter outputWriter = new BufferedWriter( + new OutputStreamWriter(outputStream)); + for (T2Reference cur : listOfReferences) { + InputStreamReader inputReader = new InputStreamReader( + getAsStream(referenceService, cur)); + IOUtils.copyLarge(inputReader, outputWriter); + inputReader.close(); + } + outputWriter.close(); + T2Reference binaryReference = referenceService + .register(outputStream.toByteArray(), 0, true, + invocationContext); + tags.put(input.getTag(), setOneInput(referenceService, + binaryReference, input)); + } else { + ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); + BufferedWriter outputWriter = new BufferedWriter( + new OutputStreamWriter(outputStream)); + for (T2Reference cur : listOfReferences) { + InputStreamReader inputReader = new InputStreamReader( + getAsStream(referenceService, cur)); + IOUtils.copyLarge(inputReader, outputWriter); + outputWriter.write(" "); + inputReader.close(); + } + outputWriter.close(); + T2Reference binaryReference = referenceService + .register(outputStream.toByteArray(), 0, true, + invocationContext); + tags.put(input.getTag(), setOneInput(referenceService, + binaryReference, input)); + } + } catch (IOException e) { + throw new InvocationException(e); + } + } + } else { + tags.put(input.getTag(), setOneInput(referenceService, t2Reference, + input)); + } + } + + /* + * submit a grid job and wait for it to finish, then get the result as + * on-demand downloads or directly as data (in case of local execution) + */ + public HashMap<String, Object> Submit(ReferenceService referenceService) throws InvocationException { + submit_generate_job(referenceService); + return submit_wait_fetch_results(referenceService); + } + + /* + * just submit the job. useful if you want to wait for it to finish later on + * + * Can the statics be made more static? + */ + public void submit_generate_job(ReferenceService referenceService) throws InvocationException { + for (ScriptInputStatic input : usecase.getStatic_inputs()) { + T2Reference ref; + if (input.getUrl() != null) { + // Does this work OK with binary + try { + ref = referenceService.register(new URL(input.getUrl()), 0, true, null); + } catch (ReferenceServiceException e) { + throw new InvocationException(e); + } catch (MalformedURLException e) { + throw new InvocationException(e); + } + } else { + ref = referenceService.register((String) input.getContent(), 0, true, null); + } + tags.put(input.getTag(), setOneInput(referenceService, ref, input)); + + } + submit_generate_job_inner(); + } + + protected abstract void submit_generate_job_inner() throws InvocationException; + + /* + * wait for a submitted job to finish and fetch the results + */ + public abstract HashMap<String, Object> submit_wait_fetch_results(ReferenceService referenceService) throws InvocationException; + + public abstract String setOneInput(ReferenceService referenceService, T2Reference t2Reference, ScriptInput input) throws InvocationException; + + protected InputStream getAsStream(ReferenceService referenceService, T2Reference t2Reference) { + Identified identified = referenceService.resolveIdentifier(t2Reference, null, null); + if (identified instanceof ReferenceSet) { + ExternalReferenceSPI ref = ((ReferenceSet) identified).getExternalReferences().iterator().next(); + return ref.openStream(invocationContext); + } + return null; + } + + public void setContext(InvocationContext context) { + this.invocationContext = context; + + } + + public InvocationContext getContext() { + return this.invocationContext; + } + + public abstract void setStdIn(ReferenceService referenceService, + T2Reference t2Reference); + + public abstract void rememberRun(String runId); + + /** + * @return the runId + */ + protected String getRunId() { + return runId; + } + + /** + * @param runId the runId to set + */ + protected void setRunId(String runId) { + this.runId = runId; + } + + /** + * @return the retrieveData + */ + protected boolean isRetrieveData() { + return retrieveData; + } + + /** + * @param retrieveData the retrieveData to set + */ + protected void setRetrieveData(boolean retrieveData) { + this.retrieveData = retrieveData; + } + + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/ExternalToolLocalInvocationMechanism.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/ExternalToolLocalInvocationMechanism.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/ExternalToolLocalInvocationMechanism.java index f846d02..e921bc4 100644 --- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/ExternalToolLocalInvocationMechanism.java +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/ExternalToolLocalInvocationMechanism.java @@ -24,8 +24,6 @@ import org.apache.taverna.activities.externaltool.manager.InvocationMechanism; import org.jdom.Element; import org.jdom.Text; -import de.uni_luebeck.inb.knowarc.usecases.invocation.local.LocalUseCaseInvocation; - /** * @author alanrw * http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationCreator.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationCreator.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationCreator.java index 8c6234d..c340f0e 100644 --- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationCreator.java +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationCreator.java @@ -23,16 +23,14 @@ import java.io.IOException; import java.util.Map; import org.apache.taverna.activities.externaltool.InvocationCreator; +import org.apache.taverna.activities.externaltool.desc.UseCaseDescription; +import org.apache.taverna.activities.externaltool.invocation.UseCaseInvocation; import org.apache.taverna.activities.externaltool.manager.InvocationMechanism; import org.apache.taverna.reference.ReferenceService; import org.apache.taverna.reference.T2Reference; import org.apache.log4j.Logger; -import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription; -import de.uni_luebeck.inb.knowarc.usecases.invocation.UseCaseInvocation; -import de.uni_luebeck.inb.knowarc.usecases.invocation.local.LocalUseCaseInvocation; - /** * @author alanrw * http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationPersister.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationPersister.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationPersister.java index b30a73b..8cc8201 100644 --- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationPersister.java +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationPersister.java @@ -22,8 +22,6 @@ package org.apache.taverna.activities.externaltool.local; import java.io.File; import org.apache.log4j.Logger; - -import de.uni_luebeck.inb.knowarc.usecases.invocation.local.LocalUseCaseInvocation; import org.apache.taverna.activities.externaltool.manager.InvocationPersister; /** http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalMechanismCreator.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalMechanismCreator.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalMechanismCreator.java index b92417c..3f95a2b 100644 --- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalMechanismCreator.java +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalMechanismCreator.java @@ -20,8 +20,6 @@ package org.apache.taverna.activities.externaltool.local; import org.jdom.Element; - -import de.uni_luebeck.inb.knowarc.usecases.invocation.local.LocalUseCaseInvocation; import org.apache.taverna.activities.externaltool.manager.InvocationMechanism; import org.apache.taverna.activities.externaltool.manager.MechanismCreator;
